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Comparative transcriptomics across the prokaryotic tree of life

Whole-transcriptome sequencing studies from recent years revealed an unexpected complexity in transcriptomes of bacteria and archaea, including abundant non-coding RNAs, cis-antisense transcription and regulatory untranslated regions (UTRs). Understanding the functional relevance of the plethora of...

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Autores principales: Cohen, Ofir, Doron, Shany, Wurtzel, Omri, Dar, Daniel, Edelheit, Sarit, Karunker, Iris, Mick, Eran, Sorek, Rotem
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987935/
https://www.ncbi.nlm.nih.gov/pubmed/27154273
http://dx.doi.org/10.1093/nar/gkw394
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author Cohen, Ofir
Doron, Shany
Wurtzel, Omri
Dar, Daniel
Edelheit, Sarit
Karunker, Iris
Mick, Eran
Sorek, Rotem
author_facet Cohen, Ofir
Doron, Shany
Wurtzel, Omri
Dar, Daniel
Edelheit, Sarit
Karunker, Iris
Mick, Eran
Sorek, Rotem
author_sort Cohen, Ofir
collection PubMed
description Whole-transcriptome sequencing studies from recent years revealed an unexpected complexity in transcriptomes of bacteria and archaea, including abundant non-coding RNAs, cis-antisense transcription and regulatory untranslated regions (UTRs). Understanding the functional relevance of the plethora of non-coding RNAs in a given organism is challenging, especially since some of these RNAs were attributed to ‘transcriptional noise’. To allow the search for conserved transcriptomic elements we produced comparative transcriptome maps for multiple species across the microbial tree of life. These transcriptome maps are detailed in annotations, comparable by gene families, and BLAST-searchable by user provided sequences. Our transcriptome collection includes 18 model organisms spanning 10 phyla/subphyla of bacteria and archaea that were sequenced using standardized RNA-seq methods. The utility of the comparative approach, as implemented in our web server, is demonstrated by highlighting genes with exceptionally long 5′UTRs across species, which correspond to many known riboswitches and further suggest novel putative regulatory elements. Our study provides a standardized reference transcriptome to major clinically and environmentally important microbial phyla. The viewer is available at http://exploration.weizmann.ac.il/TCOL, setting a framework for comparative studies of the microbial non-coding genome.
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spelling pubmed-49879352016-08-22 Comparative transcriptomics across the prokaryotic tree of life Cohen, Ofir Doron, Shany Wurtzel, Omri Dar, Daniel Edelheit, Sarit Karunker, Iris Mick, Eran Sorek, Rotem Nucleic Acids Res Web Server issue Whole-transcriptome sequencing studies from recent years revealed an unexpected complexity in transcriptomes of bacteria and archaea, including abundant non-coding RNAs, cis-antisense transcription and regulatory untranslated regions (UTRs). Understanding the functional relevance of the plethora of non-coding RNAs in a given organism is challenging, especially since some of these RNAs were attributed to ‘transcriptional noise’. To allow the search for conserved transcriptomic elements we produced comparative transcriptome maps for multiple species across the microbial tree of life. These transcriptome maps are detailed in annotations, comparable by gene families, and BLAST-searchable by user provided sequences. Our transcriptome collection includes 18 model organisms spanning 10 phyla/subphyla of bacteria and archaea that were sequenced using standardized RNA-seq methods. The utility of the comparative approach, as implemented in our web server, is demonstrated by highlighting genes with exceptionally long 5′UTRs across species, which correspond to many known riboswitches and further suggest novel putative regulatory elements. Our study provides a standardized reference transcriptome to major clinically and environmentally important microbial phyla. The viewer is available at http://exploration.weizmann.ac.il/TCOL, setting a framework for comparative studies of the microbial non-coding genome. Oxford University Press 2016-07-08 2016-05-06 /pmc/articles/PMC4987935/ /pubmed/27154273 http://dx.doi.org/10.1093/nar/gkw394 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Web Server issue
Cohen, Ofir
Doron, Shany
Wurtzel, Omri
Dar, Daniel
Edelheit, Sarit
Karunker, Iris
Mick, Eran
Sorek, Rotem
Comparative transcriptomics across the prokaryotic tree of life
title Comparative transcriptomics across the prokaryotic tree of life
title_full Comparative transcriptomics across the prokaryotic tree of life
title_fullStr Comparative transcriptomics across the prokaryotic tree of life
title_full_unstemmed Comparative transcriptomics across the prokaryotic tree of life
title_short Comparative transcriptomics across the prokaryotic tree of life
title_sort comparative transcriptomics across the prokaryotic tree of life
topic Web Server issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987935/
https://www.ncbi.nlm.nih.gov/pubmed/27154273
http://dx.doi.org/10.1093/nar/gkw394
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